Search Results - "Măndoiu, Ion I."

GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction by Al Seesi, Sahar, Al-Okaily, Anas, Shcheglova, Tatiana V, Sherafat, Elham, Alqahtani, Fahad H, Hagymasi, Adam T, Kaur, Anupinder, Srivastava, Pramod K, Măndoiu, Ion I

“…High-throughput DNA and RNA sequencing are revolutionizing precision oncology, enabling personalized therapies such as cancer vaccines designed to target…”
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Single cell RNA-seq data clustering using TF-IDF based methods by Moussa, Marmar, Măndoiu, Ion I

“…Single cell transcriptomics is critical for understanding cellular heterogeneity and identification of novel cell types. Leveraging the recent advances in…”
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Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data by Mandric, Igor, Temate-Tiagueu, Yvette, Shcheglova, Tatiana, Al Seesi, Sahar, Zelikovsky, Alex, Mandoiu, Ion I

“…This note presents IsoEM2 and IsoDE2, new versions with enhanced features and faster runtime of the IsoEM and IsoDE packages for expression level estimation…”
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Locality Sensitive Imputation for Single Cell RNA-Seq Data by Moussa, Marmar, Măndoiu, Ion I

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Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy by Sherafat, Elham, Force, Jordan, Măndoiu, Ion I

“…Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the…”
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SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis by Moussa, Marmar, Măndoiu, Ion I

“…Single-cell RNA-Seq (scRNA-Seq) is critical for studying cellular function and phenotypic heterogeneity as well as the development of tissues and tumors. In…”
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Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity by Duan, Fei, Duitama, Jorge, Al Seesi, Sahar, Ayres, Cory M, Corcelli, Steven A, Pawashe, Arpita P, Blanchard, Tatiana, McMahon, David, Sidney, John, Sette, Alessandro, Baker, Brian M, Mandoiu, Ion I, Srivastava, Pramod K

“…The mutational repertoire of cancers creates the neoepitopes that make cancers immunogenic. Here, we introduce two novel tools that identify, with relatively…”
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Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates by Al Seesi, Sahar, Tiagueu, Yvette Temate, Zelikovsky, Alexander, Măndoiu, Ion I

“…A major application of RNA-Seq is to perform differential gene expression analysis. Many tools exist to analyze differentially expressed genes in the presence…”
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Metabolic Pathway Predictions for Metabolomics: A Molecular Structure Matching Approach by Hamdalla, Mai A, Rajasekaran, Sanguthevar, Grant, David F, Măndoiu, Ion I

“…Metabolic pathways are composed of a series of chemical reactions occurring within a cell. In each pathway, enzymes catalyze the conversion of substrates into…”
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Feature selection and classifier performance on diverse bio- logical datasets by Hemphill, Edward, Lindsay, James, Lee, Chih, Măndoiu, Ion I, Nelson, Craig E

“…There is an ever-expanding range of technologies that generate very large numbers of biomarkers for research and clinical applications. Choosing the most…”
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Estimation of alternative splicing isoform frequencies from RNA-Seq data by Nicolae, Marius, Mangul, Serghei, Măndoiu, Ion I, Zelikovsky, Alex

“…Massively parallel whole transcriptome sequencing, commonly referred as RNA-Seq, is quickly becoming the technology of choice for gene expression profiling…”
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Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data by Rondel, Filipp Martin, Hosseini, Roya, Sahoo, Bikram, Knyazev, Sergey, Mandric, Igor, Stewart, Frank, Măndoiu, Ion I, Pasaniuc, Bogdan, Porozov, Yuri, Zelikovsky, Alexander

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Direct reprogramming of oligodendrocyte precursor cells into GABAergic inhibitory neurons by a single homeodomain transcription factor Dlx2 by Boshans, Linda L., Soh, Heun, Wood, William M., Nolan, Timothy M., Mandoiu, Ion I., Yanagawa, Yuchio, Tzingounis, Anastasios V., Nishiyama, Akiko

“…Oligodendrocyte precursor cells (NG2 glia) are uniformly distributed proliferative cells in the mammalian central nervous system and generate myelinating…”
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Neuraminidase subtyping of avian influenza viruses with PrimerHunter-designed primers and quadruplicate primer pools by Huang, Yanyan, Khan, Mazhar I, Khan, Mazhar, Măndoiu, Ion, Măndoiu, Ion I

“…We have previously developed a software package called PrimerHunter to design primers for PCR-based virus subtyping. In this study, 9 pairs of primers were…”
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Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data by Duitama, Jorge, Srivastava, Pramod K, Măndoiu, Ion I

“…Massively parallel transcriptome sequencing (RNA-Seq) is becoming the method of choice for studying functional effects of genetic variability and establishing…”
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Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope by Ebrahimi-Nik, Hakimeh, Moussa, Marmar, Englander, Ryan P., Singhaviranon, Summit, Michaux, Justine, Pak, HuiSong, Miyadera, Hiroko, Corwin, William L., Keller, Grant L. J., Hagymasi, Adam T., Shcheglova, Tatiana V., Coukos, George, Baker, Brian M., Mandoiu, Ion I., Bassani-Sternberg, Michal, Srivastava, Pramod K.

“…High-affinity MHC I-peptide interactions are considered essential for immunogenicity. However, some neo-epitopes with low affinity for MHC I have been reported…”
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Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development by Karunakaran, Devi Krishna Priya, Al Seesi, Sahar, Banday, Abdul Rouf, Baumgartner, Marybeth, Olthof, Anouk, Lemoine, Christopher, Măndoiu, Ion I, Kanadia, Rahul N

“…The retina as a model system with extensive information on genes involved in development/maintenance is of great value for investigations employing deep…”
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Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection by Ebrahimi-Nik, Hakimeh, Michaux, Justine, Corwin, William L, Keller, Grant Lj, Shcheglova, Tatiana, Pak, HuiSong, Coukos, George, Baker, Brian M, Mandoiu, Ion I, Bassani-Sternberg, Michal, Srivastava, Pramod K

“…Neoepitopes are the only truly tumor-specific antigens. Although potential neoepitopes can be readily identified using genomics, the neoepitopes that mediate…”
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PrimerHunter: a primer design tool for PCR-based virus subtype identification by Duitama, Jorge, Kumar, Dipu Mohan, Hemphill, Edward, Khan, Mazhar, Măndoiu, Ion I, Nelson, Craig E

“…Rapid and reliable virus subtype identification is critical for accurate diagnosis of human infections, effective response to epidemic outbreaks and…”
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Identification of mammalian orthologs using local synteny by Jun, Jin, Mandoiu, Ion I, Nelson, Craig E

“…Accurate determination of orthology is central to comparative genomics. For vertebrates in particular, very large gene families, high rates of gene duplication…”
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